Related papers: Path lengths in tree-child time consistent hybridi…
Tree-child networks are an important network class which are used in phylogenetics to model reticulate evolution. In a recent paper, Pons and Batle (2021) conjectured a relation between tree-child networks and certain words. In this short…
A communication network can be modeled as a directed connected graph with edge weights that characterize performance metrics such as loss and delay. Network tomography aims to infer these edge weights from their pathwise versions measured…
Good representations for phylogenetic trees and networks are important for optimizing storage efficiency and implementation of scalable methods for the inference and analysis of evolutionary trees for genes, genomes and species. We…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
Metrics on rooted phylogenetic trees are integral to a number of areas of phylogenetic analysis. Cluster-similarity metrics have recently been introduced in order to limit skew in the distribution of distances, and to ensure that trees in…
In evolutionary biology, phylogenetic networks are now widely used to represent the historical relationships between species and population, when this history includes reticulation events such as hybridization, gene flow and admixture…
Phylogenetic trees summarize evolutionary relationships between organisms, and tools to analyze collections of phylogenetic trees enable contrasts between different genes' ancestry. The BHV metric space has enabled the analysis of…
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…
This paper presents methods to compare high order networks, defined as weighted complete hypergraphs collecting relationship functions between elements of tuples. They can be considered as generalizations of conventional networks where only…
Rooted phylogenetic networks are often constructed by combining trees, clusters, triplets or characters into a single network that in some well-defined sense simultaneously represents them all. We review these four models and investigate…
Given a finite set $X$, a collection $\mathcal{T}$ of rooted phylogenetic trees on $X$ and an integer $k$, the Hybridization Number problem asks if there exists a phylogenetic network on $X$ that displays all trees from $\mathcal{T}$ and…
Recently there has been considerable interest in the problem of finding a phylogenetic network with a minimum number of reticulation vertices which displays a given set of phylogenetic trees, that is, a network with minimum hybrid number.…
Ancestral mixture model, proposed by Chen and Lindsay (2006), is an important model to build a hierarchical tree from high dimensional binary sequences. Mixture trees created from ancestral mixture models involve in the inferred…
The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data.…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
In recent decades, phylogenetic networks have become a standard tool in modeling evolutionary processes. Nevertheless, basic combinatorial questions about them are still largely open. For instance, even the asymptotic counting problem for…
Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data is generated by a mixture model has stimulated considerable recent…
In evolutionary studies it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between the species or their ancestors has…
Based on solid theoretical foundations, we present strong evidences that a number of real-life networks, taken from different domains like Internet measurements, biological data, web graphs, social and collaboration networks, exhibit…
Reconstructing who infected whom is a central challenge in analysing epidemiological data. Recently, advances in sequencing technology have led to increasing interest in Bayesian approaches to inferring who infected whom using genetic data…